Identifies cis-natural antisense transcripts (cis-NATs) pairs using strand-specific RNA sequencing (ssRNA-seq) data. NASTIseq provides an R package based on model comparison for characterizing the mechanism by which cis-NAT pairs regulate gene expression. This method first calculates a score based on Bayesian information criterion (BIC), and then identifies candidate cis-NAT pairs that have small intergenic distances and are on opposite strands in the genome.